You have 40 minutes for this exam. Please read it thoroughly first

26 Jun You have 40 minutes for this exam. Please read it thoroughly first

Question
Exam 3, MBB 426/726, HSCI 426; 11-3, 7 October 2011
Chapters 4 & 5; 50 points
Name: ______________________________

Student #: _________________________

You have 40 minutes for this exam. Please read it thoroughly first, and then if you have questions,
raise your hand and a TA will help you. The TA will clarify the question with the class if need be.
1. List the subdomains of (a) the IgE protein as it exists on the surface of a B cell, and of (b) an ?/? Tcell receptor, and (c) a class II MHC molecule naming the subdomains on each chain, and stating the
overall structure (number of each chain, and linkages, if any). [8 pts]

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(a) Cell surface IgE heavy chain domains:
Light chain domains:
Overall structure:

(b) T-cell receptor delta chain domains:
Gamma chain domains:
Overall structure:

(c) Class II MHC molecule domain structure:
Overall structure:

2. Answer the following questions with regions or classes of antibody. [1 pt each for 7 pts]
(a) First antibody fragment to be crystallized:_____________

Th

(b) Antibody fragment that binds antigen but has no avidity. ____________
(c) Antibody classes bearing a hinge region: _________________________

(d) Antibody class(es) comprising 4 antigen binding sites: ___________________
(e) Antibody class(es) found in tears

___________________________

(f) Antibody class(es) bearing J chains _____________________

(g) Class(es) of antibody transferred to the fetus _________________________________

https://www.coursehero.com/file/10265595/PracticeExam3-Ch0425252605/

3. The intrinsic affinity (Ka) of Antibody 1 is 106 M-1 and that of Antibody 2 is 1010 M-1. [3 pts]
(a) Which antibody binds antigen more tightly? ________________________________
(b) If the antigen for these antibodies is a repeating epitope (such as the phosphate backbone of DNA)
what would happen to their apparent affinity in switching from being an IgM to being an IgG? Would
the apparent Kd increase or decrease? Circle one.
Would it bind more tightly or more weakly? Circle one.
Explain why this is in a few words: ___________________________________________________
________________________________________________________________________________

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4. List the framework regions (FWs) and complementarity-determining regions (CDRs) of an
antibody VL domain and a T-cell receptor V? domain encoded by the following gene fragments.
[4 pts]
Antibody VL domain

Germline
V gene:
D gene:

T cell receptor V? domain

5. An antibody contacts a protein antigen at antigen residues 666, 789 and 1008. State the type of
epitope it is. ______________________________ [1 pt]

6. Circle the correct bolded word in each sentence. [2 pts]

Can ?/? T cell receptors bind to: epitopes from the surface a protein antigen, buried regions within
the protein, or both? Circle one.

Th

Can antibodies bind to: epitopes from the surface a protein antigen, buried regions within the protein,
or both? Circle one.
7. Fill in the blanks. [2 pts]
The anchor residues of a peptide antigen recognized by a CD8+ cytotoxic T cell bind to the
__________________________ domains of the _______________________ molecule.
8. Fill in the blanks. [3 pts]
CD4 on a _____________________ T cell binds mainly to the ___________________________
domain(s) of the __________________________ molecule.

9. Circle the correct term(s) written in bold. [1 pt each for 3 pts]
P nucleotide sequences can be complementary to the 5′ end / 3′ end / neither / both of a D gene.
N nucleotide sequences can be complementary to the 5′ end / 3′ end / neither / both of a J gene.
The chances of forming a correct open reading frame after VDJ or VJ joining are identical
TRUE FALSE
10. At what level (DNA, RNA, protein) is the decision to produce a cell surface antibody made? [2
pts]
RNA

PROTEIN [1 pt]

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Circle the best answer: DNA

Would this decision occur in a “naive” B cell, after antigen stimulation or both? Circle the correct
answer. [1 pt]

11. At what level (DNA, RNA, protein) is the decision to produce IgD made? [2 pts]
Circle the best answer: DNA

RNA

PROTEIN [1 pt]

Would this decision occur in a “naive” B cell or after antigen stimulation or both? Circle the correct
answer. [1 pt]

12. Regarding the recombination activating genes (RAG1 & RAG2): [Circle one; 3 pts]
(i) RAG1/RAG2 are involved in class switching. TRUE FALSE

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(ii) RAG1/RAG2 are involved in DNA ligation during recombination.

TRUE FALSE

(iii) RAG1/RAG2 are involved in creation of recombination excision circles. TRUE FALSE

13. Rearrangement at the TcR ___________________ chain locus causes the deletion of the entire
TcR _____________ chain locus

[2 pts]

14. A germline TcR beta locus comprises 100 functional V genes, 5 D genes and 4 J genes.
How many different gene-segment combinations are there, assuming no junctional diversification and
no D inversions? Using only numbers, show how you arrived at this answer.
Use scientific notation. [3 pts]
Number of different V-D-J gene-segment combinations:
How you calculated this:
If the number of different alpha chain gene segment combinations possible is 20,000, calculate the
number of different T cell receptors (i.e., V alpha –V beta combinations) that are possible:

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Number of different V alpha-V beta combinations:
15. Regarding the production of transgenic mice,

(a) From which starting genome does a transgenic mouse’s genome come from? Circle one. [1 pt]
Blastocyst , Pseudopregnant female mouse, Embryonic stem cell, The genome is a mixture
(b) Steps for making a transgenic mouse bearing a knocked out gene (KO) are listed below. Number
them in the correct order. [4 pts]
Inject ES cells into blastocyst __________

Introduce plasmid into ES cell line _______

Select clones with KO gene by PCR analysis __________
Create engineered gene fragment on a plasmid ______

Mouse with one chromosome bearing the KO _____________

Th

Chimeric offspring __________________

Mouse with two chromosomes bearing the KO ____________
Homologous recombination___________